Merge branch 'feature-c/2699-nicer-numerical-values' into 'dev'

Feature c/2699 nicer numerical values

Closes #2699

See merge request !274

browser/js/generic_axis.js

@@ -34,7 +34,7 @@ function GenericAxis (reverse, can_undefined) {
     this.values = []
     this.value_mapping = {};
     this.can_undefined = true;
-    this.NB_STEPS_IN_AXIS = 6; // Number (max) of labels per numerical axis
+    this.MAX_NB_STEPS_IN_AXIS = 8; // Number (max) of labels per numerical axis
     this.NB_STEPS_BAR = 18; // Number (max) of labels per numerical axis in histograms
     if(typeof can_undefined !== "undefined")
         this.can_undefined = can_undefined;

browser/js/numerical_axis.js

@@ -60,6 +60,10 @@ NumericalAxis.prototype = Object.create(GenericAxis.prototype);
         display_label = typeof display_label !== 'undefined' ? display_label : true;
         var self = this;
         
+        this.nb_steps = this.MAX_NB_STEPS_IN_AXIS
+        this.nb_steps_special = this.can_undefined ? 1 : 0
+        this.nb_steps_normal = this.nb_steps - this.nb_steps_special
+
         if (typeof fct === 'function') {
             this.converter = fct;
         } else {
@@ -107,12 +111,23 @@ NumericalAxis.prototype = Object.create(GenericAxis.prototype);
         else if (typeof max === 'undefined') {
             max = min + 1;
         } else {
-            min = nice_floor(min)
-            max = nice_ceil(max)
+            if (use_log)
+            {
+                min = nice_floor(min)
+                max = nice_ceil(max)
+            }
+            else
+            {
+                nice = nice_min_max_steps(min, max, this.nb_steps_normal)
+                min = nice.min
+                max = nice.max
+                this.nb_steps_normal = nice.nb_steps
+                this.nb_steps = this.nb_steps_normal + this.nb_steps_special
+            }
         }
 
         if (this.can_undefined && ! use_log) {
-            max = max + (max - min)/this.NB_STEPS_IN_AXIS
+            max = max + (max - min) / (this.nb_steps_normal)
         }
 
         this.min = min;
@@ -196,29 +211,20 @@ NumericalAxis.prototype = Object.create(GenericAxis.prototype);
                 h = h / 10;
             }
         }else{
-            var nb_steps = this.NB_STEPS_IN_AXIS-1
-            undefined_min = min
-            // Recover the initial min value
 
-            nb_steps = this.computeSteps(min, max, nb_steps);
+            this.nb_steps = this.computeSteps(min, max, this.nb_steps);
  
-            if (has_undefined) {
-                nb_steps = nb_steps -1 
-            }
-
             if (has_undefined){
                 this.labels.push(this.label("line", (this.reverse) ? 0 : 1, "?"))
-                h = (max-min)/(nb_steps+1)
-            } else {
-                h = (max-min)/(nb_steps)
             }
 
+            h = (max - min) / this.nb_steps
+
             // Computed so that pos <= 1 (in the loop below)
-            var delta = (min - max)/((min - undefined_min)/(max-undefined_min) - 1)
-            // Shift the start when there is an undefined value
-            var start_shift = (min - undefined_min)/(max-undefined_min)
-            for (var j = 0; j <= nb_steps; j++) {
-                pos = (h*j)*(1/delta);
+            var delta = max - min
+
+            for (var j = 0; j <= this.nb_steps_normal ; j++) {
+                pos = j / this.nb_steps
 
                 text = this.getLabelText(min + h*j);
                 if (this.reverse) pos = 1 - pos;
@@ -230,9 +236,10 @@ NumericalAxis.prototype = Object.create(GenericAxis.prototype);
 
     NumericalAxis.prototype.computeSteps = function(min, max, nb_steps) {
         var steps = nb_steps;
-        if (Math.abs(max - min) < nb_steps) {
-            steps = Math.abs(max - min)
-        }
+
+        // if (Math.abs(max - min) < nb_steps) {
+        //     steps = Math.abs(max - min)
+        // }
         return steps;
     }
 
@@ -264,7 +271,7 @@ PercentAxis.prototype = Object.create(NumericalAxis.prototype);
     }
 
     PercentAxis.prototype.getLabelText = function(value) {
-        return floatToFixed(value*100, 4) + "%"
+        return parseFloat(value*100).toFixed(nice_number_digits(100 * (this.max - this.min), 2)) + "%"
     }
 
 /**

browser/js/scatterPlot.js

@@ -570,6 +570,7 @@ ScatterPlot.prototype = {
         //sort each bar (axisY)
         
         this.axisY = new PercentAxis(this.m, true);
+        this.axisY.MAX_NB_STEPS_IN_AXIS = 5;
         this.axisY.init(this.m.clones, this.available_axis[this.splitY].fct);
         this.sortBarTab(this.axisY.converter);
 
@@ -1723,8 +1724,8 @@ ScatterPlot.prototype = {
      * @param {Axis} axis
      * @param {string} splitMethod
      * */
-    updateAxis: function(splitMethod, reverse) {
-        if (typeof reverse === "undefined") reverse = false;
+    updateAxis: function(splitMethod, is_Y) {
+        if (typeof is_Y === "undefined") is_Y = false;
         var axis;
         var aa = this.available_axis[splitMethod] 
         if (aa == undefined) {
@@ -1733,7 +1734,9 @@ ScatterPlot.prototype = {
         }
 
         axis = aa.axis;
-        axis.reverse = reverse;
+        axis.reverse = is_Y;
+        if (is_Y)
+            axis.MAX_NB_STEPS_IN_AXIS = 6
         axis.init(this.m.clones, aa.fct, aa.labels, aa.sort, aa.min, aa.max, aa.log, aa.display_label);
 
         return axis;

browser/js/tools.js

@@ -296,12 +296,12 @@ function floor_pow10(x)
  * nice_ceil(23.4) -> 30
  **/
 
-function nice_ceil(x)
+function nice_ceil(x, force_pow10)
 {
     if (x <= 0) return x
 
     try {
-        var floor_power10 = floor_pow10(x)
+        var floor_power10 = (typeof force_pow10 == 'undefined') ? floor_pow10(x) : force_pow10
 
         var xx = x / floor_power10
         return (xx == 1 ? 1 : xx <= 1.5 ? 1.5 : Math.ceil(xx)) * floor_power10
@@ -313,18 +313,41 @@ function nice_ceil(x)
 }
 
 
+
+/**
+ * Give a nice decimal number (to 1/2/5) above the given number
+ **/
+
+function nice_1_2_5_ceil(x)
+{
+    if (x <= 0) return x
+
+    try {
+        var floor_power10 = floor_pow10(x)
+        var xx = x / floor_power10
+        return (xx == 1 ? 1 : xx <= 2 ? 2 : xx <= 5 ? 5 : 10) * floor_power10
+    }
+    catch(e) {
+        // Always return something
+        return x;
+    }
+}
+
+
 /**
  * Give a nice decimal number under the given number
  * nice_floor(0.14) -> 0.1
  * nice_floor(23.4) -> 20
+ * nice_floor(23.4, 1) -> 23
+ * nice_floor(23.4, 100) -> 0
  **/
 
-function nice_floor(x)
+function nice_floor(x, force_pow10)
 {
     if (x <= 0) return x
 
     try {
-        var floor_power10 = floor_pow10(x)
+        var floor_power10 = (typeof force_pow10 == 'undefined') ? floor_pow10(x) : force_pow10
         return Math.floor(x / floor_power10) * floor_power10
     }
     catch(e) {
@@ -334,6 +357,43 @@ function nice_floor(x)
 }
 
 
+
+
+
+/**
+ * Give nice min/max/step numbers including the given [min, max] interval in order that steps are also nice,
+ * See examples in tools_test.js
+ * nice_min_max_steps(0.03, 19.24, 5) -> {min: 0, max: 20, step: 4}
+ * nice_min_max_steps(0, 7, 4) -> {min: 0, max:8, step: 2}
+ **/
+
+function nice_min_max_steps(min, max, nb_max_steps)
+{
+    if (min == max)
+        return {min: min, max: max, step: 0, nb_steps: 0}
+
+    var basic_step = nice_1_2_5_ceil((max - min) / nb_max_steps)
+
+    var n_min = nice_floor(min, basic_step)
+    var n_max = nice_ceil(max, basic_step)
+
+    var step = nice_1_2_5_ceil((n_max - n_min) / nb_max_steps)
+    var nb_steps = Math.ceil((n_max - n_min) / step)
+
+    // In some rare cases, we try another loop of rounding
+    var overlength = nb_steps * step - (n_max - n_min)
+    if (overlength)
+    {
+        n_min = nice_floor(min, step)
+        n_max = nice_ceil(max, step)
+        nb_steps = Math.ceil((n_max - n_min) / step)
+    }
+
+    return {min: n_min, max: n_max, step: step, nb_steps: nb_steps}
+}
+
+
+
 /**
  * Give a minimial number of digits to represent 'x' with at least 'sd' significant digits
  * nice_number_digits(14.5, 2) -> 1

browser/test/QUnit/testFiles/axis_test.js

@@ -97,7 +97,7 @@ QUnit.test("axis", function(assert) {
             0,25)
     
     assert.equal(axis.pos(m.clone(0)).pos.toPrecision(3), 0.00, "custom  : clone 0 (nlength = 0) position -> 0.00")
-    assert.equal(axis.pos(m.clone(1)).pos.toPrecision(3), 0.257, "custom  : clone 1 (nlength = 9) position -> 0.30")
+    assert.equal(axis.pos(m.clone(1)).pos.toPrecision(3), 0.30, "custom  : clone 1 (nlength = 9) position -> 0.30")
   
     //sequenceLength
     axis = new NumericalAxis(m)
@@ -107,18 +107,18 @@ QUnit.test("axis", function(assert) {
             },
             undefined,
             false)
-    
-    assert.equal(axis.pos(m.clone(0)).pos.toPrecision(3), 0.0325, "custom 2 : clone 0 (sequenceLength = 21)  position -> 0.0325")
-    assert.equal(axis.pos(m.clone(1)).pos.toPrecision(3), 0.0236, "custom 2 : clone 1 (sequenceLength = 18)  position -> 0.0236")
-    assert.equal(axis.pos(m.clone(3)).pos.toPrecision(3), 0.683,  "custom 2 : clone 3 (sequenceLength = 241) position -> 0.683")
-    assert.equal(axis.label_mapping.hasOwnProperty('0'),  false, "axis have not label 0")
-    assert.equal(axis.label_mapping.hasOwnProperty('10'), true,  "axis have label 10")
-    assert.equal(axis.label_mapping.hasOwnProperty('281'), true, "axis have label 281")
-    assert.equal(axis.label_mapping['10'].pos.toPrecision(3), 0, "pos of axis.label 10 is 0")
-    assert.equal(axis.label_mapping['281'].pos.toPrecision(3), 0.800, "pos of axis.label 281 is 0.800")
+
+    assert.equal(axis.pos(m.clone(0)).pos.toPrecision(3), 0.0700, "custom 2 : clone 0 (sequenceLength = 21)  position")
+    assert.equal(axis.pos(m.clone(1)).pos.toPrecision(3), 0.0600, "custom 2 : clone 1 (sequenceLength = 18)  position")
+    assert.equal(axis.pos(m.clone(3)).pos.toPrecision(3), 0.803, "custom 2 : clone 3 (sequenceLength = 241) position")
+    assert.equal(axis.label_mapping.hasOwnProperty('0'),  true, "axis has label 0")
+    assert.equal(axis.label_mapping.hasOwnProperty('10'), false,  "axis does not have label 10")
+    assert.equal(axis.label_mapping.hasOwnProperty('250'), true, "axis has label 250")
+    assert.equal(axis.label_mapping['0'].pos.toPrecision(3), 0, "pos of axis.label 0 is 0")
+    assert.equal(axis.label_mapping['150'].pos.toPrecision(3), 0.500, "pos of axis.label 150 is 0.500")
     assert.equal(axis.labels[0].pos, 1, "pos of axis label 0 ('?' value) is 1")
-    assert.approx(axis.labels[axis.labels.length-1].pos, 0.8, 0.01, "pos of last axis label is about 0.80")
-    assert.equal( (axis.labels.length != axis.label_mapping.length), true, "axis.labels length != axis.label_mapping length (du to '?')")
+    assert.approx(axis.labels[axis.labels.length-1].pos, 0.833, 0.01, "pos of last axis label is about 0.833")
+    assert.equal((axis.labels.length != axis.label_mapping.length), true, "axis.labels length != axis.label_mapping length (du to '?')")
 
     // sequenceLength with undefined
     axis = new NumericalAxis(m)
@@ -137,7 +137,7 @@ QUnit.test("axis", function(assert) {
     
     assert.equal(axis.pos(m.clone(0)).pos.toPrecision(3), 0.0476, "custom (percent) : clone 0 (gc = 1/21) position -> 0.0476")
     assert.equal(axis.pos(m.clone(1)).pos.toPrecision(3), 0.778, "custom (percent) : clone 1 (gc = 14/18) position -> 0.944")
-    assert.deepEqual(axis.labels[0].text,  "0.00%", "custom (percent) : check label 0.00%")
+    assert.deepEqual(axis.labels[0].text,  "0%", "custom (percent) : check label 0%")
     
     //gc + log
     axis.init(m.clones, 'GCContent', undefined, false, 0.001, 1, true)
@@ -160,7 +160,7 @@ QUnit.test("axis", function(assert) {
     axis.init(m.clones,
               function(clone) {
                   return undefined;
-              }, "V", true, 0);
+              }, "V", true, 0, 0);
     assert.equal(axis.labels.length, 2, "Just two labels: 0, undefined");
 
     // undefined values

browser/test/QUnit/testFiles/tools_test.js

@@ -46,6 +46,10 @@ QUnit.test("test rounding functions", function(assert) {
     assert.equal(nice_floor(100), 100, "rounding 100");
     assert.equal(nice_floor(451), 400, "rounding 451");
 
+    assert.equal(nice_floor(23.4), 20, "rounding 23.4");
+    assert.equal(nice_floor(23.4, 1), 23, "rounding 23.4 (base 1)");
+    assert.equal(nice_floor(23.4, 100), 0, "rounding 23.4 (base 100)");
+    
     assert.equal(nice_number_digits(42, 1), 0, "nice_number_digits 42");
     assert.equal(nice_number_digits(45.1, 2), 0, "nice_number_digits 45.1");
     assert.equal(nice_number_digits(4.51, 2), 1, "nice_number_digits 4.51");
@@ -54,6 +58,24 @@ QUnit.test("test rounding functions", function(assert) {
     }
 );
 
+QUnit.test("test nice_min_max_steps", function(assert) {
+    assert.deepEqual(nice_min_max_steps(347.34, 354.23, 10), {min: 347, max: 355, step: 1, nb_steps: 8}, "347.34..354.23 (10)");
+    assert.deepEqual(nice_min_max_steps(17, 305, 20), {min: 0, max: 320, step: 20, nb_steps: 16}, "17..305 (20)");
+    assert.deepEqual(nice_min_max_steps(17, 305, 10), {min: 0, max: 350, step: 50, nb_steps: 7}, "17..305 (10)");
+    assert.deepEqual(nice_min_max_steps(17, 305, 4), {min: 0, max: 400, step: 100, nb_steps: 4}, "17..305 (4)");
+
+    assert.deepEqual(nice_min_max_steps(190, 310, 15), {min: 190, max: 310, step: 10, nb_steps: 12}, "190..310 (15)");
+    assert.deepEqual(nice_min_max_steps(190, 310, 3), {min: 150, max: 350, step: 100, nb_steps: 2}, "190..310 (3)");
+
+    assert.deepEqual(nice_min_max_steps(0.03, 19.24, 5), {min: 0, max: 20, step: 5, nb_steps: 4}, "0.03..19.24 (5)");
+    assert.deepEqual(nice_min_max_steps(0, 7, 4), {min: 0, max: 8, step: 2, nb_steps: 4}, "0..7 (4)");
+
+    assert.deepEqual(nice_min_max_steps(43, 103, 5), {min: 40, max: 120, step: 20, nb_steps: 4}, "43..103 (5)");
+    assert.deepEqual(nice_min_max_steps(43, 103, 3), {min: 0, max: 150, step: 50, nb_steps: 3}, "43..103 (3)");
+
+    assert.deepEqual(nice_min_max_steps(42, 42, 20), {min: 42, max: 42, step: 0, nb_steps: 0}, "42..42 (20)");
+});
+
 QUnit.test("prepend_path_if_not_web", function(assert) {
     assert.equal(prepend_path_if_not_web('/tata', 'toto'), 'toto/tata');
     assert.equal(prepend_path_if_not_web('http://toto', 'toto'), 'http://toto');

browser/test/functional/test_analysis-example1.rb

@@ -26,7 +26,7 @@ class TestSimple < BrowserTest
     assert ($b.scatterplot_x_legend(0).text == "TRGV5"), "First legend should be TRGV5"
     assert ($b.scatterplot_y_legend(0).text == "TRGJ1"), "First legend should be TRGJ1"
     assert ($b.scatterplot_x_legend(0, 2).text == "119"), "First legend should be 119, it is " + $b.scatterplot_x_legend(0, 2).text
-    assert ($b.scatterplot_y_legend(0, 2).text == "0.00%"), "First legend sould be 0.00%"
+    assert ($b.scatterplot_y_legend(0, 2).text == "0%"), "First legend sould be 0%"
   end
 
   def test_02_deactivate_locus